Search

The killer-cell immunoglobulin-like receptor (KIR) gene complex, a highly polymorphic region of the human genome that encodes proteins involved in immune responses, poses strong challenges in genotyping owing to its remarkable genetic diversity and structural intricacy. Accurate analysis of KIR alleles, including their structural variations, is crucial for understanding their roles in various immune responses. Leveraging the high-quality genome assemblies from the Human Pangenome Reference Consortium (HPRC), we present a novel bioinformatic tool, the structural KIR annoTator (SKIRT), to investigate gene diversity and facilitate precise KIR allele analysis. In 47 HPRC-phased assemblies, SKIRT identifies a recurrent novel KIR2DS4/3DL1 fusion gene in the paternal haplotype of HG02630 and maternal haplotype of NA19240. Additionally, SKIRT accurately identifies eight structural variants and 15 novel nonsynonymous alleles, all of which are independently validated using short-read data or quantitative polymerase chain reaction. Our study has discovered a total of 570 novel alleles, among which eight haplotypes harbor at least one KIR gene duplication, six haplotypes have lost at least one framework gene, and 75 out of 94 haplotypes (79.8%) carry at least five novel alleles, thus confirming KIR genetic diversity. These findings are pivotal in providing insights into KIR gene diversity and serve as a solid foundation for understanding the functional consequences of KIR structural variations. High-resolution genome assemblies offer unprecedented opportunities to explore polymorphic regions that are challenging to investigate using short-read sequencing methods. The SKIRT pipeline emerges as a highly efficient tool, enabling the comprehensive detection of the complete spectrum of KIR alleles within human genome assemblies., (© 2024 Hung et al.; Published by Cold Spring Harbor Laboratory Press.)

Reprogramming of cellular energy metabolism, including deregulated lipid metabolism, is a hallmark of head and neck squamous cell carcinoma (HNSCC). However, the underlying molecular mechanisms remain unclear. Long-chain acyl-CoA synthetase 4 (ACSL4), which catalyzes fatty acids to form fatty acyl-CoAs, is critical for synthesizing phospholipids or triglycerides. Despite the differing roles of ACSL4 in cancers, our data showed that ACSL4 was highly expressed in HNSCC tissues, positively correlating with poor survival rates in patients. Knockdown of ACSL4 in HNSCC cells led to reduced cell proliferation and invasiveness. RNA sequencing analyses identified interferon-induced protein 44 (IFI44) and interferon-induced protein 44-like (IFI44L), encoded by two interferon-stimulated genes, as potential effectors of ACSL4. Silencing IFI44 or IFI44L expression in HNSCC cells decreased cell proliferation and invasiveness. Manipulating ACSL4 expression or activity modulated the expression levels of JAK1, tyrosine kinase 2 (TYK2), signal transducer and activator of transcription 1 (STAT1), interferon α (IFNα), IFNβ, and interferon regulatory factor 1 (IRF1), which regulate IFI44 and IFI44L expression. Knockdown of IRF1 reduced the expression of JAK1, TYK2, IFNα, IFNβ, IFI44, or IFI44L and diminished cell proliferation and invasiveness. Our results suggest that ACSL4 upregulates interferon signaling, enhancing IFI44 and IFI44L expression and promoting HNSCC cell proliferation and invasiveness. Thus, ACSL4 could serve as a novel therapeutic target for HNSCC., (© 2024 The Author(s). Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.)

The rhizobacterial strain BJ3 showed 16S rDNA sequence similarity to species within the Burkholderia genus. Its complete genome sequence revealed a 97% match with Burkholderia contaminans and uncovered gene clusters essential for plant-growth-promoting traits (PGPTs). These clusters include genes responsible for producing indole acetic acid (IAA), osmolytes, non-ribosomal peptides (NRPS), volatile organic compounds (VOCs), siderophores, lipopolysaccharides, hydrolytic enzymes, and spermidine. Additionally, the genome contains genes for nitrogen fixation and phosphate solubilization, as well as a gene encoding 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The treatment with BJ3 enhanced root architecture, boosted vegetative growth, and accelerated early flowering in Arabidopsis . Treated seedlings also showed increased lignin production and antioxidant capabilities, as well as notably increased tolerance to water deficit and high salinity. An RNA-seq transcriptome analysis indicated that BJ3 treatment significantly activated genes related to immunity induction, hormone signaling, and vegetative growth. It specifically activated genes involved in the production of auxin, ethylene, and salicylic acid (SA), as well as genes involved in the synthesis of defense compounds like glucosinolates, camalexin, and terpenoids. The expression of AP2/ERF transcription factors was markedly increased. These findings highlight BJ3's potential to produce various bioactive metabolites and its ability to activate auxin, ethylene, and SA signaling in Arabidopsis , positioning it as a new Burkholderia strain that could significantly improve plant growth, stress resilience, and immune function.

Human leukocyte antigen (HLA) genes play pivotal roles in numerous immunological applications. Given the immense number of polymorphisms, achieving accurate high-throughput HLA typing remains challenging. This study aimed to harness the human pan-genome reference consortium (HPRC) resources as a potential benchmark for HLA reference materials. We meticulously annotated specific four field-resolution alleles for 11 HLA genes (HLA -A , -B , -C , -DPA1 , -DPB1 , -DQA1 , -DQB1 , -DRB1 , -DRB3 , -DRB4 and -DRB5 ) from 44 high-quality HPRC personal genome assemblies. For sequencing, we crafted HLA-specific probes and conducted capture-based targeted sequencing of the genomic DNA of the HPRC cohort, ensuring focused and comprehensive coverage of the HLA region of interest. We used publicly available short-read whole-genome sequencing (WGS) data from identical samples to offer a comparative perspective. To decipher the vast amount of sequencing data, we employed seven distinct software tools: OptiType, HLA-VBseq, HISAT genotype, SpecHLA, T1K, QzType, and DRAGEN. Each tool offers unique capabilities and algorithms for HLA genotyping, allowing comprehensive analysis and validation of the results. We then compared these results with benchmarks derived from personal genome assemblies. Our findings present a comprehensive four-field-resolution HLA allele annotation for 44 HPRC samples. Significantly, our innovative targeted next-generation sequencing (NGS) approach for HLA genes showed superior accuracy compared with conventional short-read WGS. An integrated analysis involving QzType, T1K, and DRAGEN was developed, achieving 100% accuracy for all 11 HLA genes. In conclusion, our study highlighted the combination of targeted short-read sequencing and astute computational analysis as a robust approach for HLA genotyping. Furthermore, the HPRC cohort has emerged as a valuable assembly-based reference in this realm., Competing Interests: The authors declare no conflict of interest., (© 2024 The Authors.)

Urothelial carcinoma (UC) is common cancer worldwide with a high prevalence in Taiwan, especially in the upper urinary tract, including the renal pelvis and ureter, also classifying as upper urinary tract urothelial carcinoma. Here, we aim to find a representative prognostic marker that strongly correlates to this type of carcinoma. Transforming growth factor beta-1-induced transcript 1 (TGFB1I1) is a cofactor of cellular TGF-β1 and interacts with various nuclear receptors. The previous study showed that TGFB1I1 promotes focal adhesion formation, contributing to the epithelial-mesenchymal transition (EMT) with actin cytoskeleton and vimentin through TGFB1I1 regulation. We aim to reveal the role of TGFB1I1 in the tumorigenesis of UC. In silico and clinicopathological data of upper urinary tract urothelial carcinoma (UTUC) and urinary bladder urothelial carcinoma (UBUC) were accessed and analyzed for IHC staining regarding tumor characteristics, including survival outcome. Finally, an in vitro study was performed to demonstrate the biological changes of UC cells. In UTUC, overexpression of TGFB1I1 was significantly correlated with advanced tumor stage, papillary configuration, and frequent mitosis. Meanwhile, overexpression of TGFB1I1 was significantly correlated with advanced tumor stage and histological grade in UBUC. Moreover, the in vitro study shows that TGFB1I1 affects cell proliferation, viability, migration and wound healing. The EMT markers also decreased upon TGFB1I1 knockdown. In this study, we identified that TGFB1I1 regulates UC cell proliferation and viability and induces the EMT to facilitate cell migration in vitro, leading to its essential role in promoting tumor aggressiveness in both UTUC and UBUC., (© 2024 The Authors. The Kaohsiung Journal of Medical Sciences published by John Wiley & Sons Australia, Ltd on behalf of Kaohsiung Medical University.)

Background/purpose: The serpin peptidase inhibitor, clade E, member 2 (SERPINE2), is upregulated in breast cancer, prostate cancer, and urothelial carcinoma; however, limited information exists regarding its expression in oral cancer. Therefore, this study aimed to analyze the association between SERPINE2 expression and oral squamous cell carcinoma (OSCC) outcomes., Materials and Methods: SERPINE2 mRNA and protein expression in patients with head and neck squamous cell carcinoma and OSCC were investigated using online databases and tissue-array analysis. Its relationship with clinicopathological characteristics, OSCC prognosis and its biological function in OSCC cells were explored., Results: Analysis using online databases revealed higher SERPINE2 expression in tumor tissues and its role as a prognostic factor. High SERPINE2 protein levels were significantly correlated with adverse pathological parameters, including advanced clinical stage and tumor status ( P  < 0.001), lymph nodes ( P  = 0.014), and distant metastases ( P  = 0.013). High SERPINE2 expression was associated with worse overall survival ( P  < 0.001) and was identified as an independent prognostic factor for OSCC. In vitro studies revealed that SERPINE2 knockdown significantly reduced cell proliferation, migration, and invasion in OSCC cell lines., Conclusion: This study suggests that SERPINE2 may serve as a prognostic biomarker and potential therapeutic target for oral cancer., Competing Interests: The authors declare that they have no conflict of interest., (© 2023 Association for Dental Sciences of the Republic of China. Publishing services by Elsevier B.V.)

Background: Extraprostatic extension (EPE) of prostate cancer (PCa) on transrectal (TR) needle core biopsy (Bx) is a rare histopathological finding that can help in clinical decision-making. The detection efficiency of the transperineal (TP) approach is yet to be explored., Methods: We retrospectively reviewed 2848 PCa cases using concomitant systemic template biopsy (SBx) and multiparametric magnetic resonance imaging (MRI)-ultrasound fusion-targeted biopsy (TBx) using the TR (n = 1917) or TP (n = 931) approach at our institution between January 2015 and July 2022. We assessed and compared clinical, MRI, and biopsy characteristics using different approaches (TP and TR) and methods (SBx and TBx)., Results: In total, 40 EPE cases were identified (40/2848, 1.4%). TP showed a significantly higher EPE detection rate compared to TR in SBx (TR:0.7% vs. TP:1.6%; p = 0.028) and TBx (TR:0.5% vs. TP:1.2%; p = 0.033), as well as the combined methods (2.1% vs. 1.1%, p = 0.019). A significantly higher incidence of EPEs was found at non-base sites in TP than in TR (76.7% vs. 50%, p = 0.038). SBx showed a higher EPE detection rate than TBx; however, the difference was not statistically significant. TP showed higher prostate-specific antigen density (0.35 vs. 0.17, p = 0.005), higher frequency of GG4-5 in the cores with EPE (65.0% vs. 50.0%, p = 0.020), and more PCa-positive SBx cores (10 vs. 8, p = 0.023) compared to the TR., Conclusions: TP may improve EPE detection compared with TR and should be applied to patients with adverse pre-biopsy features., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Rhizobacteria from various ecological niches display variations in physiological characteristics. This study investigates the transcriptome profiling of two Bacillus subtilis strains, BsCP1 and BsPG1, each isolated from distinct environments. Gene expression linked to the synthesis of seven types of antibiotic compounds was detected in both BsCP1 and BsPG1 cultures. Among these, the genes associated with plipastatin synthesis were predominantly expressed in both bacterial strains. However, genes responsible for the synthesis of polyketide, subtilosin, and surfactin showed distinct transcriptional patterns. Additionally, genes involved in producing exopolysaccharides (EPS) showed higher expression levels in BsPG1 than in BsCP1. Consistently with this, a greater quantity of EPS was found in the BsPG1 culture compared to BsCP1. Both bacterial strains exhibited similar effects on Arabidopsis seedlings, promoting root branching and increasing seedling fresh weight. However, BsPG1 was a more potent enhancer of drought, heat, and copper stress tolerance than BsCP1. Treatment with BsPG1 had a greater impact on improving survival rates, increasing starch accumulation, and stabilizing chlorophyll content during the post-stress stage. qPCR analysis was used to measure transcriptional changes in Arabidopsis seedlings in response to BsCP1 and BsPG1 treatment. The results show that both bacterial strains had a similar impact on the expression of genes involved in the salicylic acid (SA) and jasmonic acid (JA) signaling pathways. Likewise, genes associated with stress response, root development, and disease resistance showed comparable responses to both bacterial strains. However, treatment with BsCP1 and BsPG1 induced distinct activation of genes associated with the ABA signaling pathway. The results of this study demonstrate that bacterial strains from different ecological environments have varying abilities to produce beneficial metabolites for plant growth. Apart from the SA and JA signaling pathways, ABA signaling triggered by PGPR bacterial strains could play a crucial role in building an effective resistance to various abiotic stresses in the plants they colonize.

Interstitial fibrosis assessment by renal pathologists lacks good agreement, and we aimed to investigate its hidden properties and infer possible clinical impact. Fifty kidney biopsies were assessed by 9 renal pathologists and evaluated by intraclass correlation coefficients (ICCs) and kappa statistics. Probabilities of pathologists' assessments that would deviate far from true values were derived from quadratic regression and multilayer perceptron nonlinear regression. Likely causes of variation in interstitial fibrosis assessment were investigated. Possible misclassification rates were inferred on reported large cohorts. We found inter-rater reliabilities ranged from poor to good (ICCs 0.48 to 0.90), and pathologists' assessments had the worst agreements when the extent of interstitial fibrosis was moderate. 33.5% of pathologists' assessments were expected to deviate far from the true values. Variation in interstitial fibrosis assessment was found to be correlated with variation in interstitial inflammation assessment (r 2  = 32.1%). Taking IgA nephropathy as an example, the Oxford T scores for interstitial fibrosis were expected to be misclassified in 21.9% of patients. This study demonstrated the complexity of the inter-rater reliability of interstitial fibrosis assessment, and our proposed approaches discovered previously unknown properties in pathologists' practice and inferred a possible clinical impact on patients., (© 2023. Springer Nature Limited.)

Eight gene clusters responsible for synthesizing bioactive metabolites associated with plant growth promotion were identified in the Bacillus cereus strain D1 (BcD1) genome using the de novo whole-genome assembly method. The two largest gene clusters were responsible for synthesizing volatile organic compounds (VOCs) and encoding extracellular serine proteases. The treatment with BcD1 resulted in an increase in leaf chlorophyll content, plant size, and fresh weight in Arabidopsis seedlings. The BcD1-treated seedlings also accumulated higher levels of lignin and secondary metabolites including glucosinolates, triterpenoids, flavonoids, and phenolic compounds. Antioxidant enzyme activity and DPPH radical scavenging activity were also found to be higher in the treated seedlings as compared with the control. Seedlings pretreated with BcD1 exhibited increased tolerance to heat stress and reduced disease incidence of bacterial soft rot. RNA-seq analysis showed that BcD1 treatment activated Arabidopsis genes for diverse metabolite synthesis, including lignin and glucosinolates, and pathogenesis-related proteins such as serine protease inhibitors and defensin/PDF family proteins. The genes responsible for synthesizing indole acetic acid (IAA), abscisic acid (ABA), and jasmonic acid (JA) were expressed at higher levels, along with WRKY transcription factors involved in stress regulation and MYB54 for secondary cell wall synthesis. This study found that BcD1, a rhizobacterium producing VOCs and serine proteases, is capable of triggering the synthesis of diverse secondary metabolites and antioxidant enzymes in plants as a defense strategy against heat stress and pathogen attack.

Interstitial inflammation scoring is incorporated into the Banff Classification of Renal Allograft Pathology and is essential for the diagnosis of T-cell mediated rejection. However, its reproducibility, including inter-rater and intra-rater reliabilities, has not been carefully investigated. In this study, eight renal pathologists from different hospitals independently scored 45 kidney allograft biopsies with varying extents of interstitial inflammation. Inter-rater reliabilities and intra-rater reliabilities were investigated by kappa statistics and conditional agreement probabilities. Individual pathologists' scoring patterns were examined by chi-squared tests and proportions tests. The mean pairwise kappa values for inter-rater reliability were 0.27, 0.30, and 0.26 for the Banff i score, ti score, and i-IFTA, respectively. No rater pair performed consistently better or worse than others on all three scorings. After dichotomizing the scores into two groups (none/mild and moderate/severe inflammation), the averaged conditional agreements ranged from 47.1% to 50.0%. The distributions of the scores differed, but some pathologists persistently scored higher or lower than others. Given the important role of interstitial inflammation scoring in the diagnosis of T-cell mediated rejection, transplant practitioners should be aware of the possible clinical implications of the far-from-optimal reproducibility., (© 2023. The Author(s).)

Mucinous adenocarcinoma of the urethra is extremely rare, even more so in a setting of postradiation therapy, with only 3 cases reported up to date including the first case published by our group in 2011. In the present study, we included the long-term follow-up on our previously reported case and report 3 additional cases. This is the first case series to date of this rare disease entity. The aim of this study is to review the clinicopathologic features of mucinous adenocarcinoma of the prostatic urethra in patients after receiving brachytherapy for prostatic adenocarcinoma. We identified 4 patients with a mean age of 72 years, and a mean interval of 14.8 years from brachytherapy for prostate carcinoma (grade group 1). Patients presented with hematuria or urinary retention. A colonoscopy was performed in three-fourth of patients and was within normal limits. Three patients underwent cystoprostatectomy and 1 had a transurethral resection of the prostate. On gross examination, only tumor formed a 3.5 cm tan-gray, ulcerated, friable, and necrotic mass and 2 displayed either irregular red granular or thickened areas within the prostatic urethra. Abundant extracellular mucin pools dissecting the prostatic stroma were present in all tumors, with clusters of tumor cells floating in the mucin. The mucin pools were lined by pleomorphic pseudostratified columnar mucinous epithelium. Tumors were diffusely positive for CK20, CDX2 (4/4), and AMACR (2/2); they focally expressed CK7 (2/4), and lacked nuclear β-catenin expression (3/3). PSA, PSAP, NKX3.1, p63, and GATA3 were negative in the tumors tested. Among the 3 patients who underwent radical surgery, 2 had stage 2 tumors (confined to the prostatic urethra and prostate), and 1 had a stage 3 tumor, with seminal vesicle involvement. All 4 patients were alive without disease with a mean follow-up of 4.9 years. In conclusion, brachytherapy-associated mucinous adenocarcinoma of the prostatic urethra displays intestinal-type features as its non-radiation-related counterpart. It appears to lack a villous adenoma component, displays a different immunohistochemical profile with diffuse CK20 and CDX2 positivity, and is associated with lower stage and less aggressive behavior., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Cancerous inhibitor of protein phosphatase 2A (CIP2A) is an oncoprotein overexpressed in human malignancies, including prostate cancer (PCa). In this study, we aimed to explore the oncogenic function of CIP2A in PCa cells and its underlying mechanism. We showed that 63.3% (38/60 cases) of PCa tissues exhibited a high CIP2A immunostaining, compared to 25% (3/12 cases) of BPH samples (p = 0.023). Furthermore, the protein level of CIP2A was positively correlated with patients' short survival time and nuclear AR levels in PCa tissues. Compared to PZ-HPV-7, an immortalized prostate cell line, androgen-sensitive LNCaP C-33, androgen-independent LNCaP C-81, or 22Rv1 cells exhibited a high CIP2A level, associated with high protein and phosphorylation levels of AR. While AR expression and activity modulated CIP2A expression, manipulating CIP2A expression in PCa cells regulated their AR protein levels and proliferation. The reduction of CIP2A expression also enhanced the sensitivity of PCa cells toward Enzalutamide treatment. Our data further showed that depletion of polo-kinase 1 (PLK1) expression or activity in C-81 or 22Rv1 cells caused reduced protein levels of c-Myc and AR. Notably, inhibition of PLK1 activity could abolish CIP2A-promoted expressions in c-Myc, AR, and prostate-specific antigen (PSA) in C-33 cells under an androgen-deprived condition, suggesting the role of PLK1 activity in CIP2A-promoted AR expression. In summary, our data showed the existence of a novel regulation between CIP2A and AR protein levels, which is critical for promoting PCa malignancy. Thus, CIP2A could serve as a therapeutic target for PCa., (© 2022. The Author(s).)

Background: Metformin is the most widely used drug for treating type 2 diabetes mellitus (DM), which frequently co-occurs with depressive disorders. Thus, patients with depression are likely to receive metformin. Metformin activates AMP-activated kinase (AMPK), which inhibits mechanistic target of rapamycin complex 1 (mTORC1) signaling. mTORC1 activation is essential for the antidepressant effects of ketamine and scopolamine. Thus, we hypothesized that metformin may attenuate ketamine- or scopolamine-induced antidepressant efficacies by blocking their mTORC1 activation., Methods: We assessed the acute and sustained antidepressant-like actions of ketamine and scopolamine in male Sprague-Dawley rats subjected to the forced swim test with or without metformin pretreatment. The expressions of AMPK, mTORC1, and brain-derived neurotrophic factor (BDNF) in their prefrontal cortex were assessed., Results: Metformin (50 mg/kg) attenuated the sustained, but not acute, antidepressant-like effects of ketamine (10 mg/kg) and scopolamine (25 μg/kg). Although metformin reduced mTORC1 downstream activated P70S6K, it did not significantly alter mTORser2448 activation and even increased BDNF expression. Notably, ketamine, scopolamine, and metformin all exerted significant antidepressant-like actions, as evidenced by increased AMPK phosphorylation and BDNF expression., Conclusions: Metformin-induced attenuation of sustained antidepressant-like effects are not directly dependent on AMPK-deactivated mTORC1. Our results indicate the complexity of interactions between AMPK, BDNF, and mTORC1. Further research, including mechanistic studies, is warranted to comprehensively evaluate the application of metformin in patients receiving mTORC1-based antidepressants., (© 2021. The Author(s) under exclusive licence to Maj Institute of Pharmacology Polish Academy of Sciences.)

Aims: To analyse effects and mechanisms of plant growth promotion mediated by Bacillus mycoides strain A3 (BmA3), in Arabidopsis thaliana seedlings., Methods and Results: Bacillus mycoides strain A3 (BmA3) isolated from the bamboo rhizosphere produced phytohormones, including indole-3-acetic acid (IAA) and gibberellic acid (GA), and exhibited phosphate solubilization and radical scavenging activities. A. thaliana seedlings inoculated with BmA3 exhibited an altered root architecture including an increased number of lateral roots and root hairs. Likewise, enhanced photosynthetic efficiency through the accumulation of higher levels of chlorophyll and starch, and increased plant size and fresh weight were observed in the BmA3-treated seedlings. This bacterial inoculation stimulated the antioxidant defence system by increasing the activities of catalase (CAT), guaiacol peroxidase (GPX), ascorbate peroxidase (APX) and phenylalanine ammonia-lyase (PAL). Secondary metabolites, including phenolic compounds, flavonoids and glucosinolates, were induced to higher levels in the BmA3-treated plants. Under drought and heat stresses, lower levels of H 2 O 2 , malondialdehyde (MDA) and electrolyte leakage were noticed in the treated seedlings. Genes involved in the signalling pathway of jasmonic acid (JA) including MYC2 and lipoxygenase 1 (LOX1) and salicylic acid (SA) including SAR DEFICIENT 1 (SARD1) and CAM-BINDING PROTEIN 60-LIKE G (CBP60G), and the antioxidant defence system including Ascorbate peroxidase (AtAPX) and alternative oxidase (AOX) were upregulated in BmA3-treated plants. Moreover, pathogenesis-related protein 1 (PR-1) and PR-2, marker genes for disease resistance, as well as DREB2A and HsFA2, which function in abiotic stress regulation, were also upregulated., Conclusions: BmA3 was able to activate JA and SA signalling pathways to induce plant growth and abiotic stress tolerance in A. thaliana seedlings., Significance and Impact of Study: The plant growth promotion and increased stress tolerance induced by BmA3 were the result of the combined effects of microbial metabolites and activated host plant responses, including phytohormone signalling pathways and antioxidant defence systems., (© 2021 The Society for Applied Microbiology.)

Background: Several natural products have been demonstrated to be effective in the treatment of depressive disorders. Echinacoside, a naturally occurring phenol extracted from Cistanche tubulosa, Echinacea angustifolia, and Cistanche spp, has a wide range of physiological effects, such as antioxidation, neuroprotection, anti-inflammatory, and immunoregulation, which are closely related to depression. In addition, echinacoside can activate protein kinase B (Akt), extracellular signal-regulated kinase (ERK), and brain-derived neurotrophic factor (BDNF) in the brain. A key downstream event of the Akt, ERK, and BDNF signaling pathways, namely mechanistic target of rapamycin (mTOR) signaling, plays a crucial role in generating an rapid antidepressant effect. Thus, echinacoside is a promising therapeutic agent for depression. However, research regarding the role of echinacoside in antidepressant effect and brain mTOR activation remains lacking., Materials and Methods: The forced swimming test and Western blot analysis in C57BL/6 mice was used to investigate the antidepressant-like activities of echinacoside and the underlying mechanism involved inα-amino3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR)-Akt/ERK-mTOR pathway., Results: We confirmed the suggestions by previous reports that echinacoside activates Akt/ERK signaling and further demonstrated that echinacoside could provide antidepressant-like effects in mice via the activation of AMPAR-Akt/ERK-mTOR pathway in the hippocampus., Conclusions: To the best of our knowledge, our study is the first to reveal that echinacoside is a potential treatment for depressive disorders. Moreover, the present study suggests a mechanism for the neuroprotective effect of echinacoside., (© 2022. The Author(s).)

Background and Objectives: We aimed to assess the diagnostic value of various immunohistochemical (IHC) markers and panels for differentiation among benign follicular nodules (BFNs), noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTPs), noninvasive encapsulated follicular variants of papillary thyroid carcinoma (NEFVPTCs), and infiltrative FVPTC (IFVPTC). Materials and Methods: Sixty-three cases were classified as BFNs, NIFTPs, NEFVPTCs, or IFVPTCs and were evaluated using the following markers: CK19, CD56, galectin-3, CITED1, HBME-1, VE1, and TROP-2. Results: The IHC results for NIFTP and NEFVPTC exhibited no statistically significant differences. In differentiating IFVPTCs from BFNs and NIFTPs/NEFVPTCs, galectin-3 and TROP-2 were the markers with the highest sensitivity plus high specificity, respectively. In various combinations, panel co-expression of two markers, including galectin-3 and/or HBME-1 and/or TROP-2, and the combination of galectin-3 and TROP-2 co-expression could achieve 100% in all aspects. In terms of discrimination of BFNs from NIFTP/NEFVPTC, CK19 was the single most sensitive marker (81.3%), while CD56 was the most specific (100%). The panel consisting of CK19 and/or HBME-1 exhibited the greatest sensitivity (96.9%), but the panel with CD56 and/or HBME-1 exhibited the greatest specificity (90.5%). Conclusions: Our results broaden the use of IHC markers for differential diagnoses among the four groups of follicular-based lesions. In addition, the similar IHC profiles of NIFTP and NEFVPTC also suggest the original criterion of <1% papillae within tumors, providing a reliable NIFTP diagnosis. Their close relationship may represent a spectrum of progressing neoplasia.

Recent studies have reported that SERPINE2 contributes to the development of various cancers. However, its association with urothelial carcinoma (UC) remains unclear. In this study, data on urinary bladder UC (UBUC) cases from The Cancer Genome Atlas (TCGA) database were used to investigate the prognostic value of SERPINE2 mRNA expression. Then, SERPINE2 expression was analyzed with tissue microarrays constructed from 117 upper tract UC (UTUC) and 84 UBUC tissue specimens using immunohistochemical staining. Results were compared to clinicopathologic data by multivariate analysis. In the TCGA database, high SERPINE2 mRNA expression indicated a poor prognosis in patients with UBUC. Furthermore, Mann-Whitney U test showed that high SERPINE2 immunoexpression was significantly associated with adverse pathologic parameters including invasion, high grade, coexistence of UC in situ, and advanced pT stage (all p < 0.05, except for a marginal association with high-grade UBUC, p = 0.066). Kaplan-Meier analysis revealed that high SERPINE2 expression was associated with worse overall survival (OS; UTUC, p = 0.003; UBUC, p = 0.014) and disease-free survival (UTUC, p = 0.031; UBUC, p = 0.033). Moreover, multivariate analysis identified high SERPINE2 expression as an independent prognostic factor for OS (UTUC, p = 0.002; UBUC, p = 0.024). Taken together, our findings demonstrated that increased SERPINE2 expression is associated with adverse pathologic features and may serve as a prognostic biomarker for UC.

Urothelial cancer is a malignant tumor with metastatic ability and high mortality. Malignant tumors of the urinary system include upper tract urothelial cancer and bladder cancer. In addition to typical genetic alterations and epigenetic modifications, metabolism-related events also occur in urothelial cancer. This metabolic reprogramming includes aberrant expression levels of genes, metabolites, and associated networks and pathways. In this review, we summarize the dysfunctions of glycolytic enzymes in urothelial cancer and discuss the relevant phenotype and signal transduction. Moreover, we describe potential prognostic factors and risks to the survival of clinical cancer patients. More importantly, based on several available databases, we explore relationships between glycolytic enzymes and genetic changes or drug responses in urothelial cancer cells. Current advances in glycolysis-based inhibitors and their combinations are also discussed. Combining all of the evidence, we indicate their potential value for further research in basic science and clinical applications.

Objectives: This study examined the associations between the Second-Generation Cessation Payment Scheme (SCPS) and the use of smoking cessation treatments. Furthermore, these associations were compared between light and heavy smokers in Taiwan., Design: This study had a cross-sectional design., Setting: Data were obtained from the Taiwan Adult Smoking Behaviour Surveillance System 2010-2011 and 2013-2014; data for each year consisted of a nationally representative sample of adults aged 18 years and older., Participants: Current smokers who had either quit or made a serious attempt to quit smoking were selected for the analysis., Primary Outcome Measure: The primary outcome measure was the use of a smoking cessation clinic or pharmacy in a twice daily to quit smoking., Results: According to multivariate analysis, the SCPS was positively associated with the combined use of a smoking cessation clinic and a pharmacy (OR=3.947; 95% CI: 1.359 to 11.463) when individual-level predictors (gender, age, education level, marital status, monthly household income, daily cigarette consumption, smoking status and self-reported health) were controlled. Heavy smokers showed a significant increase in the sole use of a pharmacy (OR=1.676; 95% CI: 1.094 to 2.569) and combined use of a smoking cessation clinic and pharmacy (OR=8.984; 95% CI: 1.914 to 42.173) after the SCPS was introduced. In addition, when related factors were controlled, the use of smoking cessation services was more frequent among heavy smokers than light smokers, including any treatment (OR=1.594; 95% CI: 1.308 to 1.942), a smoking cessation clinic (OR=1.539; 95% CI: 1.232 to 1.922), a pharmacy (OR=1.632; 95% CI: 1.157 to 2.302) and the combination of a smoking cessation clinic and pharmacy (OR=4.608; 95% CI: 1.331 to 15.949) ., Conclusions: The SCPS subsidisation policy increased the use of smoking cessation treatments, particularly among heavy smokers., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

The BK virus (BKV) is an emerging pathogen in immunocompromised individuals and widespread in the human population. Polymerase chain reaction is a simple and highly sensitive method for detecting BKV, but it is time consuming and requires expensive instruments and expert judgment. The lateral flow assay, a rapid, low-cost, minimal-labor, and easy-to-use diagnostic method, was successfully applied for pathogen detection. In this study, we used oligonucleotide probes to develop a simple and rapid sandwich-type lateral flow immunoassay for detecting BKV DNA within 45 minutes. The detection limit for the synthetic single-stranded DNA was 5 nM. The specificity study showed no cross-reactivity with other polyomaviruses, such as JC virus and simian virus 40. For the Escherichia coli containing BKV plasmid cultured samples, the sensitivity was determined to be 10 7 copies/mL. The approach offers great potential for BKV detection of various target analytes in point-of-care settings.

Vanillic acid, an oxidized form of vanilla, is a flavoring agent with a creamy odor. Several studies have reported the neuroprotective effects of vanillic acid, which are predominantly associated with anti-inflammatory and antioxidative properties. The anti-inflammatory and antioxidative properties may result from Akt or ERK signaling activation. The activation of the mammalian target of rapamycin (mTOR), a key downstream target of Akt and ERK signaling, is a crucial therapeutic target for treating depression. However, the antidepressant effects of vanillic acid remain unknown. The present study applied the forced swim test (FST) to investigate the antidepressant effects of vanillic acid and its association with Akt, ERK, and mTOR signaling and upstream α-amino-3-hydroxy-5-methyl-4-isoxazolepropionaic acid receptor (AMPAR) in the prefrontal cortex (PFC) of mice. Vanillic acid demonstrated antidepressant effects by significantly reducing behavioral despair in the FST. None of the treatments changed locomotor activity. Additionally, vanillic acid increased AMPAR throughput, Akt, and mTOR signaling but not ERK signaling in the PFC. NBQX (an AMPAR blocker), MK 2206 (an Akt blocker), and rapamycin (an mTOR blocker) used in pretreatment attenuated the antidepressant effects of vanillic acid, but SL327 (an ERK inhibitor) did not. The immunochemical results indicated that the antidepressant effects of vanillic acid depend on the AMPAR-Akt-mTOR signaling transduction pathway. Our findings reveal an Akt-dependent, but ERK-independent, the mechanism underlying the antidepressant effects of vanillic acid, which may be beneficial for some patients with depression., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 American Chemical Society.)

Background: Self-care is indispensable for health maintenance and well-being. This naturalistic decision-making process involves behavioral choices to maintain physiological stability (self-care maintenance) and response to occurring symptoms (self-care management). However, several factors affect self-care, but some have contradictory results., Objective: We aimed to examine how depressive symptoms, social support, eHealth literacy, and heart failure (HF) knowledge directly and indirectly affect self-care maintenance and management and to identify the mediating role of self-care confidence in self-care maintenance and management., Methods: The study included a total of 141 patients with HF (average age, 65.2 years; male, 55.3%). We analyzed their data, including demographic and clinical characteristics, obtained from the Patient Health Questionnaire-9, Multidimensional Scale of Perceived Social Support, eHealth Literacy Scale, Dutch Heart Failure Knowledge Scale, and Self-Care of Heart Failure Index. Furthermore, path analysis was conducted to examine the effects of the study variables on self-care maintenance and management., Results: Self-care confidence significantly and directly affected self-care maintenance and management and mediated the relationships between factor variables (depressive symptoms, social support, and HF knowledge) and outcome variables (self-care maintenance and management). Specifically, depressive symptoms had a negative and direct effect on self-care maintenance, whereas eHealth literacy had significant and direct effects on self-care management and HF knowledge., Conclusion: Self-care confidence decreases the negative effects of depressive symptoms on self-care. This study underscores the need for interventions targeting patients' self-care confidence to maximize self-care among patients with HF.

Puerarin is a traditional Chinese medicine with beneficial effects of reduced depression-like behaviors in mice with stress. Previous studies also show that puerarin can produce neuroprotective effect via activating the Akt or increased brain-derived neurotrophic factor (BDNF) expression. Interestingly, BDNF and Akt downstream target, mammalian target of rapamycin (mTOR) mediate the fast-acting antidepressant properties of ketamine. Until now, the involvement of the mTOR signaling pathway or BDNF on puerarin-induced antidepressant effect remains unknown. We aimed to investigate whether the antidepressant-like effect induced by puerarin would associate mTOR signaling pathway and BDNF release. The antidepressant-like effects of puerarin were evaluated using the forced swim test. The activation of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionaic acid receptor (AMPAR)-mTOR signaling pathway and release of BDNF in the prefrontal cortex were determined. We also investigated the effect of puerarin on AMPAR trafficking through measuring the PKA phosphorylation of AMPAR subunit GluR1. Our present results show that puerarin exerted antidepressant-like responses that was mediated by AMPAR-induced mTOR signaling pathway and associated with increased BDNF release. Moreover, a significant increase in the GluR1 phosphorylation at its PKA site was noted following puerarin treatment. Our findings are the first to demonstrate that the antidepressant-like actions of puerarin require AMPAR-mTOR signaling pathway activation, are associated with an increased BDNF level and facilitate AMPAR membrane insertion. These findings provide preclinical evidence that puerarin may possess antidepressant property which is mediated by the glutamatergic system.

Depression is a common issue in institutionalized elderly people. The "Attentively Embracing Story" theory is applied to help individuals transform negative thoughts into positive, and reflect on spiritual healing. This study aimed to examine the effectiveness of a "Story-Centred Care Intervention Program" based on the "Attentively Embracing Story" theory in improving depressive symptoms, cognitive function, and heart rate variability in institutionalized elderly people. Seventy long-term care residents were recruited from two long-term care facilities and randomized into the story-centred care intervention (n = 35) and control groups (n = 35). We excluded five long-term care residents who did not complete the post-test measures and five long-term care residents who had interference events on the outcome measures. Finally, sixty long-term care residents (40 women and 20 men; age 84.3±5.98 years) were included in the final analysis. Data were collected at four times (pre-intervention and post-intervention, 1 and 3-month follow-up) and analyzed with the generalized estimating equation approach.Instruments, including Geriatric Depression Scale, Short Portable Mind Status Questionnaire, and a CheckMyHeart device to measure heart rate variability, were used in study. The degree of improvement in depressive symptoms was significantly higher in the story-centred care intervention group than in the control group after providing the story-centred care intervention program (p < .001) and at 1 and 3-month follow-up (p = .001, p = .006, respectively; GDS-15 score reduced 1.816 at the 3-month follow-up). Participants receiving the story-centred care intervention program showed significantly greater improvement than those in the control group in the cognitive function at 1and 3-month follow-up (p = .009, p = .024, respectively; SPMSQ score reduced 0.345 at the 3-month follow-up). The heart rate variability parameters (SDNN, RMSSD) did not show a statistically significant increase. However an increasing trend in the parameters was observed in the intervention group (SDNN increased 16.235ms at the 3-month follow-up; RMSSD increased 16.424 ms at the 3-month follow-up). In conclusions, the story-centred care intervention program was effective on the improvement of depressive symptoms and cognitive status in institutionalized elderly people.

The dramatic increase in smartphone usage has spurred the development of many health-related mobile applications (apps). On the other hand, population aging and the associated rise in the incidence of chronic disease is increasing the demand for long-term care. Effective chronic disease self-management has been shown to help patients improve their health condition. Numerous smartphone applications currently support patient self-management of chronic disease, facilitating health management and health promotion. The purpose of the present article was to introduce the definition, contents, and types of health-related apps; to discuss the effectiveness of self-management health-related apps in promoting chronic disease management; and to assess and evaluate these apps. We hope that the present article helps give to healthcare professionals and patients who are willing to manage their diseases a general understanding of health-related apps and their potential to facilitate the self-management of chronic diseases.

Case: We present the case of a 51-year-old immunocompetent man with refractory heel pain who initially had been treated for plantar fasciitis. However, the pain was proven to be caused by a Mycobacterium abscessus infection of the calcaneus. The process of diagnosis and treatment is described., Conclusion: Although rare, chronic heel pain can be caused by an atypical mycobacterial infection of the calcaneus. Because of its indolent clinical course, misdiagnosis is not uncommon with calcaneal osteomyelitis. Physicians should note that this rare infection should be considered in patients with refractory heel pain.

Evidence indicates that the mechanisms controlling photosynthesis efficiency also regulate plant response to biotic and abiotic stress. Light-induced cell death is genetically maintained for the control of innate immunity. In a recent study we showed that the expression of AtWDR26 was induced by light, multiple plant hormones, and abiotic stress; increased AtWDR26 strongly upregulated gene groups related to chloroplast metabolism, disease resistance, and abiotic stress tolerance. Gain- and loss-of-function analyses in transgenic plants demonstrated the involvement of AtWDR26 in signaling pathways; these controls were osmotic as well as salt stress tolerance. More detailed transcriptome evidence suggested that AtWDR26 was a powerful inducer of gene expression associated with chloroplast metabolism. This included the electron transport chain of the photosystem, carbohydrate synthesis, and enzymatic activity involved in photorespiration. Moreover, genes in auxin synthesis (and perception) constituted a significant portion of those that were upregulated. Gene expression involved in disease resistance, control of cell wall flexibility, Zn uptake, and AP2/ERF transcription factors was also be upregulated. We concluded that AtWDR26 is one component in the regulatory network between light-regulated plant growth and the adaptation response to disease resistance and abiotic stress. Auxin signal acts downstream for AtWDR26 regulation and the adaptation response to biotic and abiotic stress: this occurs through modulating cell wall flexibility, Zn homeostasis, and controlling stress-related transcription factors.

Algae wall polysaccharide, laminarin (Lam), has an established role on induction of plant disease resistance. In this study, application of Lam increased Arabidopsis fresh weight and enhanced tolerance to salt and heat stress by stabilizing chloroplast under adverse environment. Transcriptome analysis indicated that, in addition to induced a large number of genes associated with the host defense, genes involved in the regulation of abiotic stress tolerance mostly the heat stress response constituted the largest group of the up-regulated genes. Lam induced expression of IRT1, ZIP8, and copper transporters involved in transport of Fe, Zn, Cu ions associated with the activity of chloroplast antioxidant system. Lam also up-regulated genes involved in the synthesis of terpenoid, a plastidial-derived secondary metabolite with antioxidant activity. Overexpression of a Lam-induced defensin like 202 (DEFL202) resulted in increased chloroplast stability under salt stress and increased plant growth activity after heat stress. Expression of antioxidant enzymes including SOD and ascorbate peroxidase (APX), photosystem PsbA-D1 and ABA-dependent responsive to desiccation 22 (RD22) was induced to higher levels in the transgenic seedlings. In sum, our results suggest that Lam is an potent inducer for induction of chloroplastic antioxidant activity. Lam affect plant abiotic stress tolerance partially through regulation of the DEFL-mediated pathway., (Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.)

The WD-40 repeat (WDR) protein acts as a scaffold for protein interactions in various cellular events. An Arabidopsis WDR protein exhibited sequence similarity with human WDR26, a scaffolding protein implicated in H2O2-induced cell death in neural cells. The AtWDR26 transcript was induced by auxin, abscisic acid (ABA), ethylene (ET), osmostic stress and salinity. The expression of AtWDR26 was regulated by light, and seed germination of the AtWDR26 overexpression (OE) and seedling growth of the T-DNA knock-out (KO) exhibited altered sensitivity to light. Root growth of the OE seedlings increased tolerance to ZnSO4 and NaCl stresses and were hypersensitive to inhibition of osmotic stress. Seedlings of OE and KO altered sensitivities to multiple hormones. Transcriptome analysis of the transgenic plants overexpressing AtWDR26 showed that genes involved in the chloroplast-related metabolism constituted the largest group of the up-regulated genes. AtWDR26 overexpression up-regulated a large number of genes related to defense cellular events including biotic and abiotic stress response. Furthermore, several members of genes functioning in the regulation of Zn homeostasis, and hormone synthesis and perception of auxin and JA were strongly up-regulated in the transgenic plants. Our data provide physiological and transcriptional evidence for AtWDR26 role in hormone, light and abiotic stress cellular events., (Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.)

Actinomycosis is a chronic disease characterized by slow progression, abscess formation, tissue fibrosis and draining sinuses. Occurrence originating from the nasopharynx is extremely low. The present study described the case of a 46-year-old otherwise healthy female, with no remarkable history of mucosal injury or teeth rottenness, who presented with an asymptomatic nasopharyngeal mass that was detected incidentally by 18 F-fluorodeoxyglucose positron emission tomography/computed tomography. A nasopharyngoscopy revealed an unclear demarcated granular mass. The patient then underwent a biopsy. Based on the obtained clinical images, microbiological results and histological findings, a diagnosis of actinomycosis was established. The patient experienced an uneventful eradication of the disease after two months of oral antibiotic treatment with amoxicillin. In conclusion, these findings indicate that actinomycosis should be included in the differential diagnosis of nasopharyngeal neoplasms.

Cavernous hemangioma of the small intestine is a rare disease in adult patients. Intussusception caused by small bowel hemangioma is extremely rare. We report a 20-year-old female presenting with lower abdominal pain and post-prandial bloating. Laboratory studies showed leukocytosis with left shifting and prominent anemia. Computed tomography of the abdomen revealed small bowel intussusception with bowel ischemia. Segmental resection of the intussuscepted jejunum was performed, and the diagnosis of cavernous hemangioma causing intussusception and anemia simultaneously was made.

Silver nanoparticles (AgNPs) are widely used as antibacterial nanomaterials; however, the environmental impacts of AgNPs remain uncertain. In this study, Arabidopsis physiological responses and gene expression were investigated after exposure to 3 different morphologies of AgNPs. The triangular (47 ± 7 nm) and spherical (8 ± 2 nm) AgNPs exhibited the lowest and highest degrees of antimicrobial activity, respectively. The AgNP-induced phenotypic alterations in Arabidopsis were correlated with nanoparticle morphology and size, in which the decahedral AgNPs (45 ± 5 nm) induced the highest degree of root growth promotion (RGP); however, the spherical AgNPs exhibited no RGP and induced the highest levels of anthocyanin accumulation in Arabidopsis seedlings. The decahedral and spherical AgNPs induced the lowest and highest levels of Cu/Zn superoxide dismutase (CSD2) accumulation, respectively. Moreover, 3 morphologies of AgNPs induced protein accumulations including cell-division-cycle kinase 2 (CDC2), protochlorophyllide oxidoreductase (POR), and fructose-1,6 bisphosphate aldolase (FBA). Regarding transcription, the AgNPs induced the gene expression of indoleacetic acid protein 8 (IAA8), 9-cis-epoxycarotenoid dioxygenase (NCED3), and dehydration-responsive RD22. Additional studies have shown that AgNPs antagonized the aminocyclopropane-1-carboxylic acid (ACC)-derived inhibition of root elongation in Arabidopsis seedlings, as well as reduced the expression of ACC synthase 7 (ACS7) and ACC oxidase 2 (ACO2), suggesting that AgNPs acted as inhibitors of ethylene (ET) perception and could interfere with ET biosynthesis. In conclusion, AgNPs induce ROS accumulation and root growth promotion in Arabidopsis. AgNPs activate Arabidopsis gene expression involved in cellular events, including cell proliferation, metabolism, and hormone signaling pathways., (Copyright © 2014 Elsevier Masson SAS. All rights reserved.)

We report the case of a 68-year-old man with a newly defined rare entity of a peripheral pulmonary tumor, consisting of a nodular papillary lesion with papillary structures containing ciliated columnar and goblet cells, as well as floating tumor cells in the mucin pool. The conspicuous mucin pool was observed to be mimicking colloid adenocarcinoma in a low-power view, particularly in a frozen section slide. We originally reported it as an adenocarcinoma during intraoperative consultation. Immunohistochemically, the tumor cells exhibited a similar immunophenotype to pulmonary adenocarcinoma, except for the presence of focal ciliated and basaloid cells, which we found using CK5/6 and P63 immunostaining. No KRAS or EGFR mutation was found. We revised the diagnosis to that of a ciliated muconodular papillary tumor (CMPT). Four years after a wedge resection, the patient remained free of tumors. Although the malignant potential of CMPT cannot be ignored, a wedge resection with a safe margin might be a treatment option for CMPT patients., (© 2014 Japanese Society of Pathology and Wiley Publishing Asia Pty Ltd.)

Plant-transformation-ready, large-insert binary bacterial artificial chromosome (BIBAC) libraries are of significance for functional and network analysis of large genomic regions, gene clusters, large-spanning genes, and complex loci in the post-genome era. Here, we report the characterization of a plant-transformation-ready BIBAC library of the sequenced Arabidopsis genome for which such a library is not available to the public, the transformation of a large-insert BIBAC of the library into tobacco by biolistic bombardment, and the expression analysis of its containing genes in transgenic plants. The BIBAC library was constructed from nuclear DNA partially digested with BamHI in the BIBAC vector pCLD04541. It contains 6144 clones and has a mean insert size of 108 kb, representing 5.2× equivalents of the Arabidopsis genome or a probability of greater than 99% of obtaining at least one positive clone from the library using a single-copy sequence as a probe. The transformation of the large-insert BIBAC and analyses of the transgenic plants showed that not only did transgenic plants have intact BIBAC DNA, but also could the BIBAC be transmitted stably into progenies and its containing genes be expressed actively. These results suggest that the large-insert BIBAC library, combined with the biolistic bombardment transformation method, could provide a useful tool for large-scale functional analysis of the Arabidopsis genome sequence and applications in plant-molecular breeding.

Harpin protein induces disease resistance in diverse plant species. Transcriptome study of tomato (Solanum lycopersicum) genome indicated that harpin activated cellular events of transcription regulation, signaling transduction, stress response, membrane transporting, photosynthesis and cell wall biosynthesis. Among the harpin-induced genes, the expression of tomato ethylene-response factor 5 (designated as SlERF5) was induced to the highest level. The amino acid sequence of SlERF5 was closely related to that of CaEREBP-C4, NtERF4 and NsERF4. Overexpression of SlERF5 in Arabidopsis thaliana activated a large number of genes involved in signaling pathways of disease resistance, redox system, abiotic response and protein phosphorylation. Seedlings of transgenic plants exhibited hypersensitive response to exogenous ABA and increased tolerance to salt stress. In summary, the results of this study suggest that SlERF5 is a transcription activator for genes involved in the responses to ABA, biotic and abiotic stress. Thus, harpin may exert its effect on plant growth and defense response through activation of SlERF5 transcription factors., (Copyright © 2010 Elsevier Inc. All rights reserved.)

Ganoderma species are white-rot fungi widespread throughout the world. In this study, a wild isolate of Ganoderma lucidum was first collected and its tolerance was tested in a medium containing 3.0 mM CdCl(2). The cDNA-amplified fragment length polymorphism method was conducted to analyze the transcription profiling of this Ganoderma species in response to Cd treatment. In total, 12 925 transcript-derived fragments (TDFs) were amplified using 256 primer combinations. Forty-nine differentially expressed TDFs were confirmed by DNA dot-blot analysis. Northern blot analysis was used to verify the transcription levels of 34 Cd-inducible TDFs. Sequence analysis indicated that genes involved in reactive oxygen species generation, synthesis of sulfur-containing metabolites, translation machinery, DNA repair, transporting system, proteolysis pathway, mitochondria function, and cell wall biosynthesis were upregulated by Cd treatment. Our results provide a genome-wide transcriptome profiling of Cd response in Ganoderma species.

Plant hormone auxin elicits diverse responses in plant growth and development. Accumulated data indicate that the ubiquitin-mediated proteolytic pathway plays a crucial role in transducing auxin signaling. To gain more understanding of the molecular mechanisms underlying auxin action, we performed a comparative transcriptome analysis of auxin responsive genes between Arabidopsis Columbia ecotype and the auxin insensitive mutant eta2 by cDNA-AFLP. Using 256 primer combinations, about 5900 transcript-derived fragments (TDFs) were amplified. Sixty-six differentially expressed TDFs were confirmed by DNA dot blot analysis. Sequence analysis indicated that, a large number of genes involved in transcription regulation or RNA metabolism were identified as auxin-regulated genes. Northern blot analyses confirmed transcription levels of 16 auxin-regulated genes. These genes include various forms of transcription regulators, defense related, RING-type ubiquitin ligases, and glycosyl hydrolase. This study demonstrates that auxin exerts its effect in complex transcriptional networks.

Auxin response in Arabidopsis thaliana requires the SCF(TIR1) ubiquitin ligase. In response to the hormone, SCF(TIR1) targets members of the auxin/indoleacetic acid (Aux/IAA) family of transcriptional regulators for ubiquitin-mediated proteolysis. To identify additional regulators of SCF(TIR1) activity, we conducted a genetic screen to isolate enhancers of the tir1-1 auxin response defect. Here, we report our analysis of the eta2 mutant. Mutations in ETA2 confer several phenotypes consistent with reduced auxin response. ETA2 encodes the Arabidopsis ortholog of human Cullin Associated and Neddylation-Dissociated (CAND1)/TIP120A, a protein recently identified as a cullin-interacting factor. Previous biochemical studies of CAND1 have suggested that it specifically binds to unmodified CUL1 to negatively regulate SCF assembly. By contrast, we find that ETA2 positively regulates SCF(TIR1) because Aux/IAA protein stability is significantly increased in eta2 mutants. Modification of CUL1 by the RUB1/NEDD8 ubiquitin-like protein has been proposed to free CUL1 from CAND1 and promote SCF assembly. We present double mutant analyses of eta2 axr1 plants indicating that liberating CUL1 from ETA2/CAND1 is not the primary role of the RUB modification pathway in the regulation of SCF activity. Our genetic and molecular analysis of SCF(TIR1) function in eta2 mutants provides novel insight into the role of CAND1 in the regulation of SCF ubiquitin-ligase activity.

The SCF(TIR1) complex is a central regulator of the auxin response pathway in Arabidopsis. This complex functions as a ubiquitin protein ligase that targets members of the auxin/indoleacetic acid (Aux/IAA) family of transcriptional regulators for ubiquitin-mediated degradation in response to auxin. In an attempt to identify additional factors required for SCF(TIR1) activity, we conducted a genetic screen to isolate enhancers of the auxin response defect conferred by the tir1-1 mutation. Here, we report the identification and characterization of the eta3 mutant. The eta3 mutation interacts synergistically with tir1-1 to strongly enhance all aspects of the tir1 mutant phenotype, including auxin inhibition of root growth, lateral root development, hypocotyl elongation at high temperature, and apical dominance. We isolated the ETA3 gene using a map-based cloning strategy and determined that ETA3 encodes SGT1b. SGT1b was identified recently as a factor involved in plant disease resistance signaling, and SGT1 from barley and tobacco extracts was shown to interact with SCF ubiquitin ligases. We conclude that ETA3/SGT1b is required for the SCF(TIR1)-mediated degradation of Aux/IAA proteins.

Abscission is a universal and dynamic process in plants whereby organs such as leaves, flowers and fruit are shed, both during normal development, and in response to tissue damage and stress. Shedding occurs by separation of cells in anatomically distinct regions of the plant, called abscission zones (AZs). During abscission, the plant hormone ethylene stimulates cells to produce enzymes that degrade the middle lamella between cells in the AZ. The physiology and regulation of abscission at fully developed AZs is well known, but the molecular biology underlying their development is not. Here we report the first isolation of a gene directly involved in the development of a functional plant AZ. Tomato plants with the jointless mutation fail to develop AZs on their pedicels and so abscission of flowers or fruit does not occur normally. We identify JOINTLESS as a new MADS-box gene in a distinct phylogenetic clade separate from those functioning in floral organs. We propose that a deletion in JOINTLESS accounts for the failure of activation of pedicel AZ development in jointless tomato plants.